Instructions for upgrading to 2.17 can be found at https://webwork.maa.org/wiki/Release_notes_for_WeBWorK_2.17#Upgrade_Instructions. I wouldn't recommend doing this during a term.
I don't recommend deleting the Contrib folder completely, since this will cause issues if you try to update the OPL in the future. It is safe to unlink Contrib from within a course as long as no Contrib problems are being used in that course. You can also delete the symlink from your model course to prevent it from being propagated to newly created courses (assuming that you are copying templates from the model course).